Targeting of integrin v3 with different sequence of RGD peptides: A molecular dynamics simulation study

Integrin alpha v133 is one of the receptors expressed in cancer cells. RGD peptides have the potential to target integrin alpha v133 (receptor), which can increase drug delivery efficiency. In this study, 55 different RGD dimer motifs were investigated. At first, the binding energy between RGD peptides and the receptor was calculated using molecular docking. Then, three RGD peptides with the strongest binding energy with the receptor were selected, and their dynamic adsorption on the receptor was simulated by molecular dynamics (MD). The obtained results showed that a sequence that has RGD at the beginning and end with tryptophan (TRP) has strong Lennard-Jones (LJ) and electrostatic interactions with Integrin alpha v133 and has changed the conformation of receptor significantly, which analyzed by root mean square deviation (RMSD) and radius of gyration.